My wife was in your situation and it can be a little confusing, especially if you are the only one affected by the plan. She had her's with Fidelity.
With a SIMPLE IRA, you, as a self-employed individual, have two "sides" of the equation to worry about, the employer side and the employee side.
On the employer side, there is the SIMPLE IRA plan where you establish the rules of the plan, establish whether you are going to do the 3% match or the 2% automatic contribution, etc.
On the employee(s) side, you open the individual investment acounts where the money will ultimately reside.
With Fidelity, there was a separate SIMPLE IRA administration web site where you, as the employer, directed the employee(s)' salary deferrals from your company bank account into their actual investment accounts.
So, for example, my wife would get her monthly check from her business activity and deposit it into her bank. Then, she would visit the SIMPLE administration site, which would have a list of all employees under her that had individual SIMPLE IRA's. In her case, she was the only one listed. She would enter the amount of the salary deferral into the box next to her name and the date the funding would take place. Then, on that date, Fidelity would EFT the specified amount from her bank account to her linked investment account.
So, the only way to fund a SIMPLE is through salary deferrals, much like a 401K at an employer.